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Informatics

User-friendly RNA-Seq analysis tools designed for biologists

RNA Sequencing Data Analysis Solutions

Intuitive Analysis of RNA-Seq Data

Once the domain of bioinformatics experts, RNA sequencing (RNA-Seq) data analysis is now more accessible than ever. Illumina offers push-button RNA-Seq software tools packaged in an intuitive user interface designed for biologists.

These user-friendly tools support a broad range of next-generation sequencing (NGS) studies, from gene expression analysis to total RNA expression profiling and more.

Intuitive Analysis of RNA-Seq Data

Benefits of RNA-Seq Data Analysis with BaseSpace Apps

RNA-Seq data can be instantly and securely transferred, stored, and analyzed in BaseSpace Sequence Hub, the Illumina genomics computing platform. BaseSpace Sequence Hub includes an expert-preferred suite of RNA-Seq software tools that were developed or optimized by Illumina. Our BaseSpace RNA-Seq Apps are:

  • Accessible to any researcher, regardless of bioinformatics experience
  • Designed to support common transcriptome studies, from transcript abundance measurement to detection of novel transcripts, coding single nucleotide polymorphisms (cSNPs), gene fusions, and more
  • Suitable for human, mouse, and rat RNA-Seq analysis (certain apps also support additional species)
  • Compatible with all Illumina sequencing systems
RNA-Seq Data Analysis FAQs

Demystifying RNA sequencing data analysis with answers to common questions and concerns.

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Key RNA-Seq Analysis Apps

Based on frequently cited RNA-Seq analysis pipelines, these apps support a broad range of transcriptome data analysis needs. Featured apps for common RNA-Seq methods are shown in the table below.

Core Lab Uses BaseSpace to Analyze mRNA-Seq Data

BRC-Seq uses BaseSpace Sequence Hub to analyze and share data (primarily mRNA-Seq data), and track samples.

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Featured Apps for RNA Sequencing Data
Method Featured App
mRNA Sequencing
Targeted RNA Sequencing BaseSpace RNA Amplicon App
Small RNA Sequencing BaseSpace Small RNA App
Learn More About RNA-Seq See All BaseSpace Apps

How to Analyze RNA-Seq Data with BaseSpace Apps

Walk through a typical BaseSpace Sequence Hub RNA sequencing data analysis workflow. Learn how to analyze your results, and view examples of the easily interpretable tables and graphs that the software generates.

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Interpretation of RNA-Seq Data

After data analysis, results can be transferred easily to BaseSpace Correlation Engine for functional annotation, to understand the biological effects of gene expression changes. BaseSpace Correlation Engine contains data sets from thousands of public studies that inform biological interpretation. Connect differential gene expression data from RNA-Seq experiments with disease associations, or visualize correlated genes and microRNA targets.

Explore BaseSpace Correlation Engine
Simplifying Genomic Data Mining

Learn how BaseSpace Correlation Engine facilitates genomic data interpretation. See examples of distinguished universities and pharmaceutical companies that have cited this tool in peer-reviewed publications.

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Additional Resources

Tale of Two RNA Library Prep Kits
A Tale of Two RNA Library Prep Kits

Comparative RNA-Seq data analysis from two TruSeq RNA kits revealed key differences in variant and fusion detection.

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